3ey1 - Revision history

OCA at 06:37, 6 September 2023

2023-09-06T06:37:00Z

←Older revision		Revision as of 06:37, 6 September 2023
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	<StructureSection load='3ey1' size='340' side='right'caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3ey1' size='340' side='right'caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp.~~ halodurans~~" boyer et al. 1973~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ey2\|3ey2]], [[3ey3\|3ey3]]</div></td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [https://pdbe.org/3ey1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [https://pdbe.org/3ey1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RNH1_BACHD RNH1_BACHD]~~] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus alcalophilus subsp.~~ halodurans ~~boyer et al. 1973~~]]	+	[[Category: Alkalihalobacillus halodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease H]]~~	+	[[Category: Egli M]]
-	[[Category: Egli, M]]	+	[[Category: Pallan PS]]
-	[[Category: Pallan~~, P S]]~~	+
-	~~[[Category: 2'-thiomethyl uridine ribonucleic acid]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Rnase h-dna complex~~]]	+

OCA at 19:48, 20 October 2021

2021-10-20T19:48:02Z

←Older revision		Revision as of 19:48, 20 October 2021
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	==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==		==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==
-	<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3ey1' size='340' side='right'caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ey2\|3ey2]], [[3ey3\|3ey3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [~~http~~://pdbe.org/3ey1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [https://pdbe.org/3ey1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	+	[[https://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/3ey1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/3ey1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]	+
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]]		[[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]]
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Egli, M]]		[[Category: Egli, M]]

OCA at 09:22, 25 October 2017

2017-10-25T09:22:57Z

←Older revision		Revision as of 09:22, 25 October 2017
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		+
	==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==		==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==
	<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://pdbe.org/3ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://pdbe.org/3ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:50, 8 February 2016

2016-02-08T07:50:11Z

←Older revision		Revision as of 07:50, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_halodurans Bacillus~~ halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://pdbe.org/3ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ey1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3ey1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
-	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus halodurans]]	+	[[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Egli, M]]		[[Category: Egli, M]]

OCA at 21:46, 24 December 2014

2014-12-24T21:46:19Z

←Older revision		Revision as of 21:46, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNH1_BACHD RNH1_BACHD]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
		+	*[[Temp\|Temp]]
		+	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 41:
	[[Category: Bacillus halodurans]]		[[Category: Bacillus halodurans]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
-	[[Category: Egli, M.]]	+	[[Category: Egli, M]]
-	[[Category: Pallan, P S.]]	+	[[Category: Pallan, P S]]
	[[Category: 2'-thiomethyl uridine ribonucleic acid]]		[[Category: 2'-thiomethyl uridine ribonucleic acid]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 13:11, 29 September 2014

2014-09-29T13:11:01Z

←Older revision		Revision as of 13:11, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3ey1.~~png~~\|~~left~~\|200px]]	+	==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==
		+	<StructureSection load='3ey1' size='340' side='right' caption='[[3ey1]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EY1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ey2\|3ey2]], [[3ey3\|3ey3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnhA, BH0863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ey1 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/3ey1_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

-	~~{{STRUCTURE_3ey1\| PDB=3ey1 \| SCENE= }}~~	+	A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.,Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M Chem Commun (Camb). 2009 Apr 21;(15):2017-9. Epub 2009 Feb 26. PMID:19333476<ref>PMID:19333476</ref>

-	~~===A Conformational Transition in~~ the ~~Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19333476}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ey1]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_halodurans Bacillus halodurans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019333476<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus halodurans]]		[[Category: Bacillus halodurans]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]

OCA at 09:27, 20 October 2012

2012-10-20T09:27:20Z

←Older revision		Revision as of 09:27, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ey1]] is a 2 chain structure ~~of [[Ribonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].	+	[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].

	==See Also==		==See Also==

OCA: Protected "3ey1" [edit=sysop:move=sysop]

2012-07-25T22:54:04Z

Protected "3ey1" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:54, 25 July 2012

OCA at 22:54, 25 July 2012

2012-07-25T22:54:03Z

←Older revision		Revision as of 22:54, 25 July 2012
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-	{{Seed}}
	[[Image:3ey1.png\|left\|200px]]		[[Image:3ey1.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3ey1\| PDB=3ey1 \| SCENE= }}		{{STRUCTURE_3ey1\| PDB=3ey1 \| SCENE= }}

	===A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution===		===A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution===

-
-	<!--
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	{{ABSTRACT_PUBMED_19333476}}		{{ABSTRACT_PUBMED_19333476}}

	==About this Structure==		==About this Structure==
-	~~3EY1~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].	+	[[3ey1]] is a 2 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19333476~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019333476</ref><references group="xtra"/>
	[[Category: Bacillus halodurans]]		[[Category: Bacillus halodurans]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
Line 29:		Line 20:
	[[Category: Pallan, P S.]]		[[Category: Pallan, P S.]]
	[[Category: 2'-thiomethyl uridine ribonucleic acid]]		[[Category: 2'-thiomethyl uridine ribonucleic acid]]
-	[[Category: Cytoplasm]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/dna complex]]	+	[[Category: Hydrolase-dna complex]]
	[[Category: Magnesium]]		[[Category: Magnesium]]
	[[Category: Manganese]]		[[Category: Manganese]]
Line 39:		Line 29:
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Rnase h-dna complex]]		[[Category: Rnase h-dna complex]]
-	[[Category: X-ray crystallography]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:27:03 2009''

OCA at 06:27, 6 May 2009

2009-05-06T06:27:04Z

←Older revision		Revision as of 06:27, 6 May 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3ey1.~~jpg~~\|left\|200px]]	+	[[Image:3ey1.png\|left\|200px]]

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	[[Category: X-ray crystallography]]		[[Category: X-ray crystallography]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 30 10~~:08:18 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:27:03 2009''